the way i start te firmware is with the WOOD.nds file which I start in the original firmware.
the main firmware on my itouch2 is 3.9a
memory card is a kingstond microsd 4gb class 4
memory space free is 153 mb.

I have reformatted my Memory card already and put the same files back and the problem still occurs after that. I tried several games with no result, but Homebrew like
lameboy and lmp-ng ( an ipod mp3-player lookalike homebrew) seem to work fine.
in the first weeks of using the firmware i had no problems with it, only when i moved some files on the memory card, moonshell and some anime in .dpg files, the problems began to occur. I don't know if there is a relation between these things, because after deleting all these files that I moved onto my memory card, the problem still occurs.
so does anyone know how to solve this? could it be that I somehow have to reset manually my memory or something? ( sorry if it sounds stupid)

*edit*
i have found something on the internet, that says if that this message is shown that it simply doesn't have DLDI support, but nds games aren't supposed to be have DLDI support right? that was only for homebrew i thought. so i think that he sees al my files as homebrew and try to do something with DLDI when i start a game or homebrew, and that's why only homebrew work I think, but still no solution for this problem.
games still loads somehow when i start YSMenu.nds(had put on my microsd later). it simply starts the game immediately when i start ysmenu.nds. it seems that it's always the last file i opened with the woodys firmware. but this time it works, so there is a solution, but not the most time-saving one.

I remember, to avoid DLDI confusion (iTouch uses iTDS and R4iRTS uses R4_I, not M3DS), ysm3.nds's dldi region is locked. I suppose it is completely safe to launch the game from ysm3.

[edit] Do you mean you don't see YSM3 at all and "ini linker" freezes in rebooting?
There is a boot chain: WoodYS(aka WAIO) -> rpglink(white char on black screen) -> inilink(white char on yellow screen) -> YSM3 (black screen with black-metallic progress bar) -> game

WOODys starts boots up normal. when i start a game, not homebrew, its says a lot of stuff, something of initializing dldi etc. and at the end this message appears. when i start with YSmenu the last opened rom with wood starts. this is a glitch that is already fixed. this was a known issue. i tried the new version of 6.74, but it didn't help.
it struck me as strange that it said reboot and stopped working.

i have tried another microsd , kingston class 4 , 8gb, with 2 gb free space. just copied the same woodys firmware that was on my other micro sd onto this one and it worked
as it should.
i have tried also ysmenu from woodys 6.74 which booted normally on the 4 gb micro sd. so i think i can say that the problem idd occurs in that cycle.

YSM3.nds works fine i think. the screen where the message occured was dark-blue/black with white letters, dont know which one in the boot chain it was,
the load bar of ysmenu dont appear.
in the log that is visible on the screen it says arm7 copyfrom and copyto then that arm7 is loaded,
then again 3 lines of information that says copyfrom and copyto and then that arm9 is loaded.
then :
Dynamically linked disk interface patch to oL v1.24 by Michaell Chisholm (chism)

then something about based on revision 1.4 (which doesn't look suspicious to me so i don't mention it here)

based on the information you gave i would say the problem is with RPGlink.

i would like to add that the wood firmware had worked as it should so it is something that started after some time.

*edit*
(after seeing your account description i think you actually are the right person to help me )

anyway,
after doing like you said i got another problem...
it says at the end :
Cannot open /MOONSHL2/EXTLINK/_hn.HugeNDSLoader.nds.
Accept your fate.
press A to shutdown.

i did change the entry from
[mshl2wrap]hbmode = 1M3DS = /TTMenu/inilink.nds
to
[mshl2wrap]hbmode = iTDS = /TTMenu/inilink.nds
and
[mshl2wrap]hbmode = 1iTDS = /TTMenu/inilink.nds
and
iTDS = /TTMenu/inilink.nds
and
1iTDS = /TTMenu/inilink.nds
all of them showed the message.

*edit*

problem solved :

the problem was the loader.eng file. which wasn't a specific file from the WOODys (secondary )firmware, but from my primairy firmware .
I used a the normal WOODys 6.74 firmware and the normal ItouchDS 3.9a firmware from filetrip. I don't what exactly the problem was, but it is solved now
maybe the file was already corrupt in my backup, that's probably the reason it didn't worked.

can finally continue playing 9 hours 9 persons 9 doors

i was thinking, why is moonshell needed to boot when using the firmware? moonshell is used to play music and/or movies. I don't remember it could play games.
anyway problem solved.

ok, but I won't make other edits now in my firmware because it is now working fine. the problem was with my primairy firmware loader. though I could play games with my primairy firmware, I couldn't with the secondary firmware which was booted from my primairy. I don't know what the real problem was, but it had nothing to do with moonshell after all. I used the orginal mshl2wrap.ini.

anyway, it is good to hear that there was another problem found and can be solved.
my file editing skills aren't that great ( almost zero ) and I still don't know what you mean with :

bah inilink.ini linebreak is LF? Use notepad++ stuff to edit... not windows notepad. Or you can edit using MoonShell2...